Innovative metabolic reprogramming in rice: unlocking drought resilience through microbial consortia interaction and sustainable agriculture

Abstract

Rice is a global staple food facing climate change challenges, such as drought, salinity, alkalinity, and heat stress. Proteomics, genomics, gene expression, and metabolic changes use adaptation strategies, but translating them into field conditions remains a challenge. This review highlights the role of microbial consortia in drought adaptation, crop resilience, and food security through several drought mitigation strategies. Plants use a “cry for help” strategy to restructure their microbiome, alleviate stress, and improve health and nutrition. Understanding the complex feedback between microbes and plants is crucial for future crop drought resilience. Microbial consortia eliminate stress, such as drought stress, by acclimatizing plants to various tactics, enhancing water uptake. Techniques like UPLS/GC detect profiling and plant growth regulators influenced by microbial consortia under water scarcity. Metabolomics can identify secondary metabolites, chemical signaling, and governing systems in plant groups, contributing to drug development and drought tolerance in cereal crops, such as rice and wheat. Key microbial consortia candidates have been identified for nitrogen-fixing bacteria, phosphate-solubilizing bacteria, mycorrhizal fungi, phytohormones, siderophores, and biofortifying crops with nutrients, such as zinc. Future research is needed to understand molecular pathways and identify microbial species that improve drought tolerance. Key challenges include addressing drought effects on plants, understanding plant–microbial consortia functions, and advancing multiomics, synthetic communities (SynComs), and host-mediated microbiome engineering for drought-resilient agriculture.

Introduction

Plants and endophytic micro-organisms flourish under natural field conditions, where microbial consortia have the potential to boost crop production and enhance resilience against biotic and abiotic stresses (Jan et al. 2024). The metabolites, which are by-products of gene and protein regulation, play a crucial role in influencing the phenotype of rice (Zeng et al. 2021). Metabolomics, transcriptomics, and quantitative trait loci (QTLs) are distinct biological analysis methods that offer unique insights into cellular processes. QTLs are specific regions on a chromosome linked to variations in a trait, such as height or disease susceptibility. Transcriptomics studies RNA transcripts, revealing genes active in response to specific conditions. Metabolomics analyzes small molecules within a biological system, revealing downstream consequences of gene expression. Combining these methods provides a comprehensive understanding of biological pathways and regulatory mechanisms, enabling a more holistic understanding of complex biological processes. Non-targeted metabolomics can shed light on the variations observed among different rice varieties (Zhao et al. 2022). Transcriptome sequencing provides valuable information on gene expression (Guo et al. 2024). In addition, QTLs offer a molecular foundation for the improvement of rice quality (Jiang et al. 2024).

Abiotic stresses such as drought, cold stress, and salinity pose significant economic risks to rice cultivation, with drought directly impacting the growth and development of rice crops (Korres et al. 2017; Soualiou et al. 2022; Hassan et al. 2023). The application of microbial consortia in semi-arid conditions has shown promise in mitigating these challenges, reducing water loss, and enhancing the morphological, physiological, biochemical, and metabolic activity of rice plants (Mondal et al. 2020; Abd El-Mageed et al. 2022; Navarro-Torre et al. 2023). Research indicates that UV-B radiation has a significant impact on rice yield and quality globally, revealing notable differences in metabolite accumulation between the indica and japonica rice subspecies. Furthermore, it identifies critical genes associated with UV-B response, such as OsMYB44, which is linked to UV-B tolerance, and OsUVR8, which is involved in flavonoid synthesis, thereby providing insights into crop responses and adaptation (Zhang et al. 2024a). A comprehensive approach combining both targeted and untargeted metabolomics identified 246 metabolites in both japonica and indica rice seeds. Japonica rice exhibited higher levels of sugars, alanine, flavonols, and luteolin complexes, whereas the indica rice showed increased concentrations of organic acids, amino acids, flavanones, and apigenin (Tian et al. 2024).

Microbial consortia alleviate stresses on rice plants by modulating various morphological, physiological, biochemical, and metabolic functions, which ultimately reduces water loss and enhances water uptake. These consortia are known to induce changes in the morphological structure of rice plants. They secrete compounds, such as lignin and gum, which affect the opening and closing dynamics of natural plant openings, such as stomata, lenticels, and hydathodes. In addition, they are involved in the metabolic and biochemical processes by influencing metabolomics and protein synthesis under drought conditions (Beattie 2006; Nunes da Silva et al. 2022). Research has identified eight drought-tolerant bacterial strains from the rice rhizosphere that significantly improve drought resistance in rice crops. These bacteria exhibit growth-promoting characteristics and contribute to enhanced seedling growth and vigor index. Their inoculation could serve as an effective bioinoculant strategy to address water scarcity and food security challenges in fluctuating climatic conditions (Mahreen et al. 2023). Microbial consortia are essential for activating and boosting the production of both primary (carbohydrates, nucleic acids, amino acids, lipids, and plant growth regulators) and secondary metabolites (phytic acid, atropine, cyanogenic glucoside, and flavonoids) (Fig. 1) (Zhang et al. 2018; Castiglione et al. 2021; Das et al. 2022; Koza et al. 2022). The microbial consortium activates the rice defense system by triggering primary and secondary metabolites under biotic and abiotic stress conditions. Primary metabolites balance defensive proteins, plant hormones, and lipids. Secondary metabolites induce biochemical and physiological changes through the activation of ecto- and endo-mycorrhiza and plant growth-promoting rhizobacteria (PGPRs), such as Rhizobacteria, Azotobacter, and Azospirillium (Fig. 1).

Fig. 1.

Microbial consortium activates the defence system in rice plants by triggering primary and secondary metabolites under biotic and abiotic stress conditions. Primary metabolites balance a diverse group of defensive proteins, plant hormone cascade signalling, and a complex group of lipids, such as phospholipids, lignin, and phenolic compounds, through the defence mechanisms in plants under stress conditions by inducing modulation. Secondary metabolites (such as antibiotics, siderophores, and phytohormones) induce biochemical and physiological changes through the activation by ecto- and endo-mycorrhiza, along with PGPRs (such as Rhizobacteria, Azotobacter, and Azospirillum)

Our primary focus has been on the significant role and necessity of microbial consortia in mitigating drought stress. With the rise in global temperatures and the increasing risk of drought, it is imperative to develop innovative strategies to minimize its impact on plant health (González-Pérez et al. 2022; Menon et al. 2024). Drought currently affects 64% of the Earth's land area, and plants have developed adaptive mechanisms to conserve water and reconfigure their molecular responses. In drought conditions, microbial consortia present in plant roots regulate hormonal signaling, influence proteomic dynamics, activate oxidative stress defenses, form compatible solutes, and modify plant growth regulators (Upadhyaya and Panda 2019; Chieb and Gachomo 2023). These microbial consortia, as a diverse group residing in the rhizosphere and endosphere, establish symbiotic relationships that help mitigate drought stress (Del Carmen Orozco-Mosqueda et al. 2022; Aloo et al. 2023; Kaushal et al. 2023). Their crucial contributions include elicitation of jasmonic acid (JA) and salicylic acid (SA), as well as their interlinked pathways with plant growth regulators, which collectively enhance the growth and resilience of rice plants (Dhakarey et al. 2017; Chen et al. 2022; Parwez et al. 2022; Nandy et al. 2023).

The exploration of plant interactions with microbial consortia reveals their essential role in promoting the growth of rice plants amid drought conditions. These consortia are involved in various processes, including the signaling pathways associated with plant growth regulators, regulation of drought-responsive gene expression, activation of the PAMP (Pathogen Associated Molecular Pattern) system, and the development of plant root systems (Khati 2017; Nephali et al. 2020; Zargar et al. 2022; Gowtham et al. 2024). These microbial partnerships produce key plant hormones that enable rice plants to adjust their water uptake in response to abiotic stress.

This review highlights improvements in water uptake efficiency, modifications in genes associated with abiotic stress, and the activation of defense mechanisms, underscoring the significance of microbial consortia in water-deficit conditions (Poudel et al. 2021; Lee et al. 2024). The review delves into the interplay between microbial elicitation and plant growth regulators, particularly focusing on Abscisic acid (ABA), cytokinins (CK), Ethylene (ET), and auxins under drought and biotic stress circumstances in rice, revealing insights into how plants respond to water scarcity (Khan et al. 2021). In addition, the review examines the influence of plant microbial consortia on genomic and amino acid transformations during water scarcity. It identifies changes in protein structure and function, reprogramming of metabolites, and the intricate dynamics of interactions, highlighting the complexity of micro-organisms' roles in plant stress responses (Kyndt et al. 2012).

The research gap lies in the complex interplay between water uptake efficiency, gene modification under stress conditions, and plant defense mechanisms. This review highlights the significance of microbial consortia under water deficit conditions, playing a pivotal role in enhancing plant resilience. It addresses existing research gaps concerning the function of microbial consortia as bio-stimulants under drought stress, their influence on hormonal signaling cascades, their acclimatization to abiotic challenges, methods for detecting hormone production through ultra-performance liquid chromatography, their impact on plant proteomics, drought resilience, soil health, and their role in hormonal signaling and drought resilience.

Metabolic profiling and microbial consortia for symbiotic relationships as bio-stimulants under drought stress

Secondary metabolism in plants plays a vital role in producing metabolites that contribute to their biological functions, particularly in survival and defense mechanisms. The integration of metabolomic technologies and bioinformatics is essential for data analysis. NMR spectroscopy serves as a pivotal tool for identifying stress-responsive markers. A recent study focused on the metabolome of rice plants vulnerable to Meloidogyne graminicola, utilizing NMR Mass spectrometry-based metabolomics. This research identified a total of 100 significant metabolites—48 upregulated and 52 downregulated—as well as key biomarkers, shedding light on plant–nematode interactions and strategies for managing root knot (Gautam et al. 2024).

Fatty acids: Investigations into rice metabolomics are integral for biomarker development and pharmacology research, supporting sustainable development goals. GC–MS profiling of two rice varieties, Kullkar and Milagu Samba, unveiled 144 differential metabolites. The resulting OPLS–DA predictive model enriched three metabolic pathways: fatty acid biosynthesis, beta-oxidation of very long-chain fatty acids, and plasmalogen synthesis, thereby enhancing the functional and nutritional significance of rice grains (Subramanian et al. 2024). Fatty acid synthesis and plasmalogen synthesis are carried out using autotrophic–heterotrophic consortia (Liu et al. 2020) and Clostridium perfringens (Jackson et al. 2021), respectively.

Phenolics: Research on the probiotic fermentation of nine brown rice varieties, including FBR-1741, highlighted their richness in polyphenolic metabolites. Polyphenolics may enhance bioactive metabolites and their effectiveness against obesity-related target proteins. This intervention was found to improve lifespan, reduce triglycerides, and suppress the expression of fat-related genes in human beings (Barathikannan et al. 2024). A study develops a microbial consortium that improves plant productivity, nutritional value, and soil health by utilizing Enterobacter hormaechei and Brevundimonas naejangsanensis strains. This consortium mitigates the pathogenic effects of the blast disease-causing fungus Pyricularia oryzae by reprogramming primary metabolites to enhance the concentration of lignin, silica, and phenolic compounds, such as catechuic and protocatechuic acid (Deng and Naqvi 2019). The consortium demonstrated improvements in growth attributes, yields, and enzyme activity in chickpea seeds under drought stress conditions in rice.

Flavonoids: A study leveraging LC–MS-based metabolite profiling examined nutrient and bioactive metabolites in various colored rice grains, identifying a total of 1,292 metabolites, including five specific flavonoid compounds. The differential regulation of flavonoid and cofactor biosynthesis pathways was observed, with black rice exhibiting the highest levels of bioactive flavonoids, followed by red rice (Zhao et al., 2024b). In addition, findings indicate that the purple rice variety YZ6H displays superior antioxidant properties compared to other colored rice grains. Key antioxidant capacity indices identified in this analysis included phorizin, trans-3,3ʹ,4′,5,5′,7-hexahydroxyflavanone, and trilobatin. These compounds are essential for maintaining a balanced diet and enhancing the nutritional value of rice (Zhu et al. 2024). The compound phorizin (3 OH) has been significantly produced by Bacillus megaterium (CYP102A1) from apples via hydroxylation (Nguyen et al. 2021); however, phorizin and trilobatin can be produced non-significantly from purple and black rice through genetic engineering (Zhu et al. 2024).

Signaling molecules: A cold-triggered OsHPL1 gene, belonging to the CYP74 family, significantly alters rice metabolism. This alteration leads to the accumulation of 12-oxo-phytodienoic acid (OPDA) and jasmonates in wild-type plants while also reshaping lipid and amino acid metabolism in rice mutants (Wu et al. 2023c). Nunna and Sai (2024) report that rice landraces and cultivars play an influential role in the activity of microbial consortia under varying moisture conditions, including water scarcity. These influences are observed through changes in soil chemical and biochemical properties, soil carbon content, enzymatic activity (such as urease, phosphatase, and dehydrogenase), microbial biomass, and respiratory activity within the rhizosphere. Their study highlights a notable decline in the populations of Firmicutes and Bacteroidetes within the rhizosphere of the Norungan landrace, alongside an increase in Acidobacteria, Actinobacteria, Chloroflexi, and Proteobacteria. Conversely, the root zone of the high-yielding variety (HYV) Co51 exhibited an increased population of rhizospheric Firmicutes and Bacteroidetes while observing a decline in Acidobacteria and Proteobacteria under conditions of water scarcity.

Microbial consortia significantly improve crop production and agricultural product nutritional value. They contribute to ecosystem sustainability by reducing pesticide use, fostering increased productivity, functioning as biocontrol, and enhancing nutrient availability. They also enhance drought tolerance and resilience to abiotic stress, thereby improving the nutritional quality of crop products (Tabacchioni et al. 2021; Carneiro et al. 2023). Symbiotic relationships primarily involve the synthesis of symbiosis-specific proteins, with proteomics revealing the functions of rhizobia in legumes and their implications for plant proteomics (Larrainzar and Wienkoop 2017; Zenda et al. 2021). Understanding the dynamics of plant proteomics, hormonal signaling pathways, and microbial consortium interactions under drought stress is essential. It elucidates how these consortia bolster plant resilience against drought and uncovers the complex molecular mechanisms at play during water scarcity (Othibeng 2022). Microbial mixtures, known as plant bio-stimulants, are marketed under various names, such as amino acids, humic acid, fulvic acid, seaweed extract, synthetic oligo-groups, and essential elements (such as Si, Cu, Co, Se, and Na) (Van der Weide et al. 2022). They enhance crop production, nutritional quality, and agricultural ecosystem balance by minimizing chemical inputs and restoring balance (Bulgari et al. 2019).

Plant roots regulate water and nutrient absorption, with RSOsPR10, a pathogenesis-related protein, being induced by drought and salinity in rice, engaging the JA, ET, and SA pathways (Takeuchi et al. 2011). The threats posed by climate change to rice growth necessitate the implementation of strategies such as stomatal closure, modifications in root development, manipulation of plant hormones, and genetic engineering to enhance drought tolerance (Aslam et al. 2022). Studies focus on mitigating drought stress in rice by altering cellular activities, including chemical, biochemical, molecular, and metabolic changes, as well as the synthesis of signaling hormones, specifically SA and JA (Dhakarey et al. 2017; Sasi et al. 2021). Metabolomic studies show a rise in antioxidant compounds within pigmented rice varieties. Microbial consortia maintain plant metabolites, enhancing crop production, nutritional value, ecosystem balance, and drought tolerance. Plant bio-stimulants also improve crop productivity and ecological balance. Rice landraces and cultivars influence the activity of microbial consortia in response to moisture and water scarcity conditions. The key research gap lies in the understanding of precise mechanisms by which microbial consortia interact with metabolic pathways. Under drought stress, these consortia regulate stress-responsive genes and rewire plant molecular machinery, improving rice quality. Using microbial consortia under semi-arid conditions decreases water loss and increases water uptake in plants. For instance, some fungal and bacterial consortia involved in plant metabolomics are given below.

Plant metabolomics and fungal and bacterial consortia under symbiotic relationship under drought stress

Microbial consortia, including fungi, bacteria, actinomycetes, and viruses, are found on plant surfaces and can be categorized into systemic and non-systemic groups. Their presence and behavior depend on their interactions with plants and their life cycles (Berendsen et al. 2018; Odoh et al. 2020). Microbial consortia exhibit various interactions, including symbiosis, parasitism, hyperparasitism, mutualism, and antagonism. Over time, these consortia have co-evolved with plants, influencing nutrient availability and plant growth regulators. Factors such as genotypic diversity and environmental conditions also play crucial roles in these dynamics (Dutilloy et al. 2022; Hajji-Hedfi et al. 2025).

A metabolomic analysis comparing rice genotypes IR64 and Azucena reveals that Azucena compensates for environmental challenges by enhancing root system growth and surface area, while IR64 adapts through increased cell wall thickness. Azucena's metabolic pathways are enriched in shikimate synthesis, fatty acid biosynthesis, purine metabolism, the tricarboxylic acid (TCA) cycle, and amino acid biosynthesis, while IR64 demonstrates heightened activity in starch and sucrose metabolism (Ghorbanzadeh et al. 2023). Microbial consortia are prevalent within the rhizosphere and phyllosphere of plants, occupying areas, such as the upper surfaces of roots, leaves, flowers, and seeds (Chialva and Bonfante 2018; Murphy et al. 2019). These consortia contribute to enhanced nutrient availability by facilitating nitrogen synthesis in root nodules, converting insoluble phosphorus into soluble forms, and reclaiming contaminated soils. They comprise diverse groups, such as Rhizobium, Mycorrhiza, Pseudomonas fluorescens, Azospirillum, Azotobacter, Actinomycetes, PGPRs, and endophytes (Odoh et al. 2020). Among bacterial groups, Actinobacteria, Rhizobacteria, and Pseudomonads can colonize the internal tissues of plants. In addition, endophytic fungi from the genus Trichoderma serve as biocontrol agents, antagonists, and phosphorus solubilizers (Singh et al. 2022). Molecular and metabolic interactions between various rice genotypes and microbial consortia enable their coexistence across diverse environmental and soil conditions. They enhance nutrient acquisition and activate defense systems against phytopathogens, such as Pyricularia oryzae, which causes rice blast disease (Vishwakarma et al. 2020; Modi and Jha 2022).

A metabolomic study has identified a QTL on chromosome 11 associated with bacterial leaf blight (BLB) in rice, with the mutant line T1247 showing resistance. The study identified four differentially expressed genes (DEGs) and 37 resistance analog genes, revealing the mechanisms of BLB resistance in rice (Ma et al. 2023). The CBB23 rice variety, containing the Xa23 resistance gene, revealed 7997 DEGs, including several cloned rice anti-blight genes upregulated in rice infected leaves. The study also identified 431 differentially expressed transcription factors. The study also found a reduction in alkaloid and terpenoid content following inoculation with Xanthomonas oryzae (pv. Oryzae) strain AH28 (Chen et al. 2024b). Microbial consortia can strengthen nutrient acquisition, defense against phytopathogens, and promote overall plant growth.

Plant metabolomics and hormonal signal cascades modulated by microbial consortia during drought stress

Plants utilize various metabolic pathways, including amino acids, for their growth and cellular functions. Elevated CO₂ levels can enhance nitrogen metabolism and energy metabolism components, leading to positive outcomes for glutamine, asparagine, and methionine levels in shoots and roots. This phenomenon supports the idea of CO₂-based gaseous fertilization as an energy-efficient strategy for rice cultivation (Li et al., 2024). A metabolomic analysis of six indica rice seeds in China revealed significant concentrations of amino acids, sugars, and organic acids. NX rice seeds provide advantages for carbohydrate and fat metabolism and sustaining growth, while CH seeds are better suited for glycine supplementation. NX seeds exhibit higher levels of glutenin and gliadin, and the lactulose content in NX seeds may not be suitable for individuals with diabetes (Zhou et al. 2024). In response to drought stress, the plant participates in a signaling cascade involving hormones that are regulated through interactions with microbial consortia (Chieb and Gachomo 2023). The interplay between these consortia and hormonal pathways under water-deficit conditions in field crops has been a focus of recent research, highlighting their role in initiating signaling and sensory responses to enhance resilience against drought stress (Wu et al., 2023b). The understanding of how multifaceted signaling pathways contribute to mitigating drought stress in rice is significantly evolving (Zhang and Kuster 2019). Microbial consortia promote the growth and development of rice plants by improving nutrient availability, modulating plant growth regulators, inducing metabolic changes, and activating defense mechanisms under drought conditions (Sanglard et al. 2016). They can enhance the biomass of rice plants by reprogramming ABA synthesis and accumulating antiseptic compounds in drought-affected plants (Lakshmanan et al. 2016; Sun et al. 2023). Drought stress directly impacts rice crop productivity; thus, employing microbial consortia presents a promising and effective approach to manage this challenge (Jha et al. 2013; Upadhyaya and Panda 2019; Khan et al. 2021). Under water scarcity, these consortia facilitate numerous processes related to water regulation in rice plants, including the synthesis of ACC (1-aminocyclopropane-1-carboxylate) activity, deaminase enzymes, polysaccharide, the production of eruptive metabolic compounds (EMC), specific amino acids, and free-radical scavengers that enhance mineral nutrient availability, phytohormones and stimuli (Shahrajabian et al. 2022; Zheng et al. 2023). Collectively, these mechanisms help to fortify plants against drought stress through mycorrhizal consortia in rice crops, while simultaneously promoting growth and nutrient uptake, aiding in the transformation of mucilage and amino acids for plant cell development.

Modern “omics technologies” have shown that beneficial fungi and bacteria stimulate signal transduction and alter metabolomic profiles (Shi et al. 2013), which are crucial for the communication and defense mechanisms of plants (Awasthi et al. 2021; Ghate et al. 2022). Understanding gene expression and interactions between plants and microbes can provide insights into the activation of plant immune responses, virulence traits, and overall dynamics of plant–microbe interactions (Liu et al. 2015). PGPRs and mycorrhizae are fundamental contributors to agricultural productivity by stimulating the availability of essential nutrients and reprogramming plant growth regulator pathways for improved drought tolerance. Expanding research on microbial consortia is highly advisable (Xu and Fu 2022). Integrating bacteria with traits for plant growth promotion or abiotic stress resistance could enhance drought tolerance and increase the accumulation of medicinal compounds in plant roots.

Climate variability, including drought, heat stress, salinity, cold stress, and pesticide toxicity, is significantly affecting rice cultivation across various environments (Chen et al. 2021b; Hasanuzzaman et al. 2023). Primary plant metabolites, such as phenolics, lignin, and phytohormones, play a crucial role in managing these natural challenges. The presence of reactive oxygen species (ROS), such as oxygen free radicals (O₂⁻), hydrogen peroxide (H₂O₂⁻), nitrite (NO₂⁻), and nitric oxide (NO⁻), can lead to detrimental effects on the nucleic acids and protein structures within rice plant cells. Pathogenesis-related (PR) proteins, which are produced and restructured in response to stress, are essential for managing these challenges (Baysal et al. 2020).

Plants undergo a reprogramming process to combat water scarcity, triggered by secondary metabolites, such as phytic acids, atropine, cyanogenic glucosides, flavonoids, SA, and JA (Elshafie et al. 2023). SA and JA play pivotal roles in the signaling pathways that activate defense mechanisms in rice plants facing drought stress (Ali and Baek 2020; Jiang et al. 2020). In response to drought conditions, plants regulate hormonal levels, improve nutrient availability, and activate various defense systems. In addition, microbial consortia play a significant role in managing water scarcity by producing polysaccharides and facilitating plant growth.

A significant research gap exists in the specific molecular mechanisms and gene networks involved in reprogramming processes. A comprehensive understanding of these reprogramming processes, characterized by gene expression and the interactions between plants and microbes, is essential for developing sustainable agricultural practices and enhancing drought tolerance. Integrating beneficial bacteria with plant growth promotion strategies or resistance to abiotic stress can further enhace drought resilience and the accumulation of medicinal compounds. This review reveals the intricate relationships between changes in the plant proteome and microbial colonization during drought stress. It emphasizes the role of microbial mediation at the interface of hormonal signaling, proteomic shifts, and metabolomic changes. Insights gained from this research bring the development of sustainable agricultural strategies and enhance drought resilience through microbiota-mediated mechanisms, ultimately transforming agriculture to meet the challenges posed by increasing drought conditions.

Role of microbial consortia in salicylic acid (SA) activation during abiotic stress acclimatization

Microbial consortia activate various metabolic and proteomic responses in plants, yielding significant effects on the signaling and sensing pathways triggered by SA and JA. These responses facilitate the modulation of proteins and hormonal mechanisms, including ABA, CK, ET, and auxins, particularly under drought and biotic stress conditions in rice (Liang et al. 2017; Khan et al. 2023). As a natural signaling molecule, SA is integral to plant defense mechanisms during stressful situations. It regulates key metabolic functions, such as photosynthesis, metabolite accumulation, and gene expression (Nadarajah et al. 2021). Additional research is warranted to further dissect the SA-responsive pathways and the mechanisms underlying abiotic stress tolerance.

Impact of microbial consortia on jasmonic acid (JA) for enhancing rice plant metabolites and grain quality

In drought conditions, rice plants adapt by downregulating typical chemical, biochemical, metabolic, and physiological activities through signaling and sensing pathways influenced by SA and JA. This leads to reduced respiration and transpiration, regulating the osmotic pressure in rice cell walls (Khan et al. 2023). The upregulation of the OsWRKY76 gene contributes to abiotic stress responses, bolstering cold tolerance and drought resilience through JA signaling transduction (Zhang et al. 2023).

A recent study using metabolomics and transcriptomics identified the amino acid pathway as a significant differentiator, serving as a potential biomarker, between premium and second-best rice varieties, with 42 gene expressions and 11 metabolites essential for the development of premium rice (Wang et al. 2024a). Microbial metabolism in SuiJing 18 rice revealed substantial alterations in rice quality Linked to reduced nitrogen fertilizer application. Key sweet volatile compounds, such as 4-methyl-benzeneacetaldehyde, Hexyl acetate, and 2-methylnaphthalene, were present at elevated levels, contributing to distinct flavor profiles (Wu et al. 2024).

Plants in their root zones undergo mutualistic relationships with microbial consortia, including fungi and bacteria. Particularly, PGPRs significantly affect the levels of JA, facilitating the modulation and reprogramming of plant growth regulators (Islam et al. 2024). Microbial consortia exhibit antagonistic properties against phytopathogenic fungi in sunflower crops, both under wet and dry conditions. The potential for bio-priming microbial consortia to regulate JA levels and alleviate water scarcity challenges in field crops has been supported by prior studies. For instance, Kim et al. (2020) isolated a drought-resistant strain of Variovorax sp. YNA59, which promotes broccoli growth while lowering JA levels, highlights its possible role as a microbial consortium to enhance crop resilience under semi-arid conditions. Siraj et al. (2022) identified a rhizobacterial strain AGH3, obtained from Achyranthes aspera L. and Calotropis procera. The study demonstrated the ability to increase plant height and mitigate defense mechanisms triggered by water deficits, showcasing its applicability in organic farming practices. Analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that rice response to UV-B stress through the regulation of phenylpropanoid, tyrosine, and tryptophan biosynthesis, with the OsMYB44 gene, is functionally important in rice (Zhang et al. 2024b). The rhizospheric microbial assembly is shaped by interactions among microbes and plants, where glucosinolates play a pivotal role. The alpha-diversity of bacterial/archaeal populations affects the overall community composition (Chroston et al. 2024). Key metabolic pathways and their roles in the reprogramming of rice metabolic flux are summarized in Table 1.

Table 1.

Rice metabolic flux reprogramming under plant stress and functions of key metabolic pathways

Key metabolic pathways over-presented in rice	No. of metabolites (pval < 0.01) (Wanichthanarak et al. 2020))	Key functions in rice metabolic reprogramming	References
ABC transporters	138	The study reveals that OsABCG18, a rice ATP-binding cassette transporter, is crucial for long-distance root-derived cytokinin transport. Cytokinins are essential for plant life processes. Overexpression of OsABCG18 increased cytokinin levels in the shoot, improving grain yield Seed development is crucial for plant reproduction and yield, with OsABCI15 and OsABCI16 genes involved in rice grain-filling. Overexpression enhances seed-setting rate and yield OsABCG36, a G-type transporter, is involved in Cd tolerance in rice	Zhao et al. 2019; Ma et al. 2024; Fu et al. 2019
Alanine, aspartate, and glutamate metabolism	28	The metabolism reveals that salt-tolerant rice cultivars show increased expression of GABA synthesis genes, which is crucial for salt-stress tolerance. By raising endogenous ABA and GABA contents, improving osmotic adjustment, antioxidant defences, and ion balance, exogenous GABA administration increases salt-stress tolerance	Feng et al. 2024
Aminoacyl-tRNA biosynthesis	52	Yellow leaf chlorosis (YLC3), a rice thermo-sensitive mutant, reduces chlorophyll content, alters thylakoid structure, and increases free aspartate, asparagine, and glutamine levels in leaves under low temperature conditions. It activates aminoacyl-tRNA biosynthesis, regulating amino acid metabolism and chloroplast thylakoid development. Aminoacyl-tRNA synthetases mutants in tobacco, Arabidopsis, and rice disrupt amino acid homeostasis and chloroplast development	Ostersetzer-Biran and Klipcan 2020
Phenylalanine, tyrosine, and tryptophan biosynthesis	35	The role of aromatic amino acids (AAA) in protein synthesis, metabolism, and secondary metabolites, including pigment compounds, plant hormones, and biological polymers is very crucial. AAA metabolism is significantly correlated with host–pathogen interactions, gut bacteria, and herbicides and antibiotics Vascular plants, like grasses, synthesize lignin and phenylpropanoids from phenylalanine and tyrosine, producing tyrosine faster than Arabidopsis while maintaining high production of these compounds	Parthasarathy et al. 2018 El-Azaz et al. 2023
Cyanoamino acid metabolism	45	Cyanide (CN −) assimilation in plants occurs through β-cyanoalanine synthase (β-CAS) and sulfotransferase (ST), converting CN − into thiocyanate (SCN −). Exogenous SCN − was applied to rice plants, causing increased CN − and SCN − content, but not with SCN − alone. The SCN − application alters gene expressions associated with β-CAS and ST, inducing β-cyanoaline synthesis pathway	Ullah et al. 2023
Glyoxylate and decarboxylate metabolism	62	The study investigates Bacillus pumilus LZP02's role in promoting rice root growth through proteomic, transcriptomic, and metabolomic techniques, revealing it enhances rice ion absorption, peroxidase activities, chlorophyll content, and upregulates carbohydrate metabolism genes, increasing glyoxylate and dicarboxylate metabolism	Liu et al. 2020
Secondary metabolites-part-2	73	Bacterial endophytes are gaining interest as a therapeutic alternative, producing unique secondary metabolites with anti-microbial, antiviral, anti-cancer, and anti-inflammatory properties, offering immense biotechnological possibilities. Modern genomic tools reveal plant–endophyte interactions, revealing new bioactive secondary metabolites, such as alkaloids, benzopyrones, and tannins	Narayanan and Glick 2022
Arginine biosynthesis	23	Rice roots require OsASL1 gene for water, nutrient uptake, and environmental sensing. Expression patterns vary, with OsASL1 gene encoding argininosuccinate lyase, mainly in roots and localized to cytosol and nucleus	Xia et al. 2014
Valine, leucine, and isoleucine biosynthesis	23	Branched chain amino acids (BCAAs) regulate energy, nutrition, gut health, immunity, and disease, and can be biomarkers for diseases, such as insulin resistance, T2DM, cancer, and cardiovascular diseases	Nie et al. 2018
Glucosinolate biosynthesis	77	Rhizosphere microbial community assembly is influenced by microbe–microbe–plant interactions, with glucosinolates shaping community composition through breakdown products and plant nitrile-specifier proteins, impacting colonization and bacterial alpha-diversity which is dependent upon functional nitrile-specifier proteins and glucosinolate biosynthesis pathways	Chroston et al. 2024
Glutathione metabolism	38	This metabolism plays a multifunctional regulation in rice, including stress-induced metabolic changes in varieties Baldo and Vialone Nano, under salt stress. Results show differential regulation of cell-cycle progression and cell-death patterns at the root level, highlighting the role of ROS and antioxidative pathways in the redox network in rice	Cimini et al. 2022
Citrate cycle (TCA cycle)	20	The TCA cycle is a crucial plant metabolism pathway, allowing controlled growth and photosynthesis changes. Enzymes can improve performance and postharvest properties. Mitochondria are vital for growth, cell maintenance, respiration, amino acid biosynthesis, nitrogen metabolism, and cellular redox homeostasis	Zhang and Fernie 2023
Taurine and hypotaurine metabolism	22	By boosting the survival rate under salt stress, rice overexpressing the OsDRAP1 gene enhances salt tolerance. This is primarily because it enriches genes involved in taurine and hypotaurine metabolism as well as amino acid production Excess manganese in plants can negatively impact growth and development. Taurine, an amino acid with antioxidant and anti-inflammatory properties, has been investigated for its potential in plant metal stress tolerance. Taurine upregulated antioxidant enzyme activities, improved growth, and reduced Mn content in Mn-stressed plants	Wang et al. 2021a, b; Hafeez et al. 2022
Glycine, serine, and threonine metabolism	50	L-serine biosynthesis in plants depends on atmospheric CO2 concentration, with Phosphorylated Pathway of Ser Biosynthesis (PPSB) affecting carbon, nitrogen, and sulphur metabolism. Overexpression of PPSB increases Ser, amino acids, protein, and starch levels	Casatejada-Anchel et al. 2024

Microbial consortia triggering cytokinins (CK) for reprogramming rice plant metabolites

Cytokinin, a class of plant hormones, regulates growth and development processes, including cell division, differentiation, senescence, and responses to stress. Microbial consortia have been identified as significant contributors to the production of CK and their reprogramming, particularly under water stress conditions, resulting in varied physiological and molecular responses (Dhatt et al. 2019). CK produced by PGPR can enhance drought tolerance in various crops. Certain strains, like Pseudomonas fluorescens G20-18, can elevate CK levels, thereby improving water scarcity tolerance through the activation of the plant defense system and the synthesis of secondary metabolites, including hydrogen cyanide (HCN) and di-phluroglucamic acid (2,4-DPGA). İpek and Mutluay (2022) investigated the influence of ammonia-oxidizing bacteria (AOB) on corn. They reported that inoculation of plants with Acinetobacter pittii improved growth parameters post-rewatering through ammonification processes occurring in the rhizosphere. In a controlled rain-shelter pot experiment, the AOB strain S2_8_1 was observed to positively impact both growth metrics and CK concentrations, promoting compensatory growth and enhancing drought resilience in rice (Kamada-Nobusada et al. 2013). Rice sheath blight (RSB) resistance is linked to the CYT02 gene, a member of the CYP450 subfamily. This gene enhances resistance and promotes vegetative tillering in rice, likely through the regulation of plant CK synthesis, the production of ROS, and the synthesis of phytoalexins (Zheng et al. 2024). The involvement of microbial CK in modulating plant responses to drought stress through physiological and molecular mechanisms underscores the need for further research. Understanding the influence of CK on hormonal signaling pathways could lead to improved rice health through comprehensive, structural, and functional reprogramming by various microbial consortia under drought stress (Sun et al. 2020; Wu et al. 2023a).

Microbial consortia and their role in modulating abscisic acid (ABA) pathways for reprogramming rice plant metabolism

Microbial consortia play a fundamental role in influencing molecular hormonal signaling mechanisms. They activate the mitogen-activated protein (MAMP) signaling cascade, particularly under drought stress conditions in rice (Kishi‐Kaboshi et al. 2010; Fukushima et al. 2020). The plant growth regulator ABA regulates key physiological activities, proteomics, and metabolomics. It impacts root development, regulates the timing of stomatal opening and closing, and modulates gene expression in response to drought (Zhang et al. 2020). Wei et al. (2013) indicate that microbial consortia can transform and modulate the signaling and sensing processes related to plant growth regulators, mitigating the effects of water deficit under challenging conditions (Chen et al. 2023). Microbial consortia in Arabidopsis maintain chlorophyll levels by modulating ABA signaling during drought stress (Daszkowska-Golec 2016). A schematic diagram of hormone–microbe interactions triggering SA, NO, ABA, and JA pathways is presented in Fig. 2.

Fig. 2.

Interactive representation of hormone–microbe interactions demonstrates the role of salicylic acid, nitric oxide, abscisic acid, and jasmonic acid in signaling cascades. Micro-organisms, including fungi and bacteria, can activate jasmonate (JA) pathways in plants, enhancing their virulence against necrotrophic pathogens, binding to the JAZ proteins, and triggering gene expression. They can also produce abscisic acid (ABA) or influence it, impacting plant responses to abiotic stress (drought, salt, and cold). Salicylic acid (SA) is a key hormone in defense against pathogens and environmental stress in plants. Pseudomonas, Bacillus, Azospirillum, Salmonella, Achromobacter, Vibrio, Yersinia, Mycobacteria, Streptomyces, Sclerotinia, Aspergilli, and Trichosporon influence SA pathways. SA is synthesized from chorismate via isochorismate. Nitric oxide (NO)-influencing micro-organisms play a role in UV damage recovery, biofilm formation, protection from oxidative stress, pathogen virulence, and oxygen regulation. Plant stress responses involve complex biochemical pathways, including pyrabactin resistance (PYR) and related genes, which interact with regulatory components of the abscisic acid (ABA) receptor. Protein phosphatase 2C (PP2C) acts as a negative regulator, while ABA activates Sucrose nonfermenting 1 (SNF1)-related protein kinase 2 (SnRK2) enzymes. The slow anion channel (SLAC) is involved in cellular ion fluxes, and Abscisic acid-responsive factors (ABFs) activate gene expression in response to ABA. The jasmonate pathway is another key signaling route, with JAZ5 acting as a repressor protein, AOC and LOX3 involved in jasmonate biosynthesis, and JAR1 important for jasmonate conjugation. Enhanced disease susceptibility 5 (EDS5) is involved in salicylic acid (SA) signaling, while AVRPPHB susceptible 3 is another genetic factor. Small archaeal modifier proteins (SAMPs) are involved in bacterial gene regulation, and calcium-dependent protein kinases (CDPKs) are crucial regulators of plant defense

Figure 2 illustrates that plant stress responses involve intricate biochemical pathways. Pyrabactin resistance (PYR) and its related genes like PYR1 interact with regulatory components of the abscisic acid (ABA) receptor. Protein phosphatase 2C (PP2C) acts as a negative regulator in this system. Sucrose nonfermenting 1 (SNF1)-related protein kinase 2 (SnRK2) enzymes are activated by ABA. The slow anion channel (SLAC) is involved in cellular ion fluxes. Abscisic acid-responsive factors (ABFs) are transcription factors to activate gene expression in response to ABA. The jasmonate pathway is another key signaling route. Jasmonate ZIM-Domain 5 (JAZ5) is a repressor protein in this pathway. Allene oxide cyclase (AOC) and Lipoxygenase 3 (LOX3) are enzymes involved in jasmonate biosynthesis. Jasmonate resistance 1 (JAR1) is important for jasmonate conjugation. Enhanced disease susceptibility 5 (EDS5) is involved in salicylic acid (SA) signaling. AVRPPHB susceptible 3 is another genetic factor. Isochorismoyl glutamate synthase (IGS) is an enzyme in the SA pathway. Non-expresser of pathogenesis-related protein 4 (NPR4) influences defense gene expression. Small archaeal modifier proteins (SAMPs) are involved in bacterial gene regulation. Calcium-dependent protein kinases (CDPKs) are important regulators of plant defense. Enhanced Pseudomonas susceptibility 1 (EPS10) is linked to bacterial interactions, and calmodulin (CaM) mediates calcium signaling (Fig. 2). Invaders trigger the transcriptional regulation of signaling molecules, such as SA, NO, JA, ABA, and polyamines, to regulate downstream genes and strengthen defense responses (Rai et al. 2021).

Micro-organisms can activate jasmonate (JA) pathways to enhance plant defense against necrotrophic pathogens. Microbes bind to JAZ proteins and trigger downstream gene expression. Microbes can produce or alter abscisic acid (ABA) levels, impacting plant adaptation to abiotic stresses, such as drought, salt, and cold. Salicylic acid (SA) is a vital hormone that governs plant defense against pathogens and environmental stress. Numerous micro-organisms that influence SA pathways include Pseudomonas, Bacillus, Azospirillum, Salmonella, Achromobacter, Vibrio, Yersinia, and Mycobacteria, Streptomyces, Sclerotinia, Aspergilli, and Trichosporon. SA synthesis starts from chorismate and proceeds through isochorismate. Micro-organisms that influence NO pathways are diverse. NO signaling is linked to UV damage recovery, important for biofilm formation, and protects from oxidative stress. NO also impacts pathogen virulence and regulates oxygen. These interconnected pathways highlight the complex interplay between plant physiology and the microbial world (Fig. 2).

Drought is a critical factor impacting crop productivity, as it leads to degradation of the photosynthetic apparatus, disrupts metabolic pathways, and promotes the generation of reactive oxygen species (ROS). Under drought conditions, phytohormones such as ABA and auxins are instrumental in enhancing drought tolerance (Mekureyaw et al. 2022). The synergistic interaction between plant hormones and microbiota is essential for improving plant resilience to drought stress (see Fig. 3). Microbial consortia, comprising Pseudomonas fluorescens, arbuscular mycorrhizal fungi (AMF), and Trichoderma spp., positively impact plant growth and fitness under biotic and abiotic stress conditions. They activate the rice defense system, modulate phytohormone levels, and enhance root development and nutrient uptake. These consortia also influence root architecture and plant growth regulators and metabolites under drought conditions in rice (Fig. 3). For instance, Bacillus subtilis (LDR2), a well-known PGPR, enhances wheat photosynthetic efficiency and alters hormonal dynamics, resulting in elevated levels of indole-3-acetic acid (IAA) while lowering ABA and ACC concentrations (Mearaji et al. 2021). Such alterations in hormonal dynamics and regulatory pathways significantly influence plant responses. Yan et al. (2022) identify Bacillus megaterium BOFC15 as a strain that releases spermidine, a polyamine known to enhance biomass in Arabidopsis, improve root structure, and boost photosynthetic efficiency. This has been correlated with increased ABA levels, further enhancing drought

Fig. 3.

Microbial consortia, including plant growth-promoting rhizobacteria (PGPR) Pseudomonas fluorescens, endophytic fungi arbuscular mycorrhizal fungi (AMF), and Trichoderma spp., have a synergistic and beneficial effect on plant growth and fitness under specific conditions of biotic and abiotic stress, activating the defense system, modulating phytohormone levels, and enhancing root development and nutrient uptake. Pseudomonas fluorescence and Trichoderma spp. both activate the rice defence system, enhancing plant growth and nutrient uptake, through the secretion of organic acids, leading to the conversion of insoluble tri-phosphates into soluble mono-phosphates. Microbial consortia have their synergistic influence on the advancement of root architecture, and modulate plant growth regulators and plant metabolites under drought conditions in rice

Understanding the relationship between plant-associated microbial consortia and the ABA signaling pathway is crucial for optimizing plant responses to drought stress. Future research efforts should focus on elucidating the collaborative interactions among microbiota, the significance of microbial-derived metabolites, and the sustainable strategies for microbiota manipulation. Such insights can equip farmers with the knowledge necessary to cultivate crops that exhibit improved drought resilience.

Microbial consortia modulating ethylene for reprogramming rice plant metabolites

Ethylene, a significant plant hormone, imparts plant development, maturity, and adaptation to stress. Drought conditions pose a substantial threat to plant vigor and productivity. PGPRs have been shown to influence ET signaling pathways. A study demonstrates that the rice ET-insensitive mutant MHZ3 enhances the stability of the OsEIN2 gene by interacting with its Nramp-like transmembrane domain. This interaction significantly hinders the process of protein ubiquitination and obstructs proteasome-mediated protein degradation, thereby highlighting its critical role in ET signaling pathways (Ma et al. 2018). Similarly, another study confirms that MHZ3 (MaO HU ZI 3, a stabilizer of ET receptor) assists in the phosphorylation of OsCTR2, influencing various aspects of plant growth, development, and stress responses in rice. However, when rice plants are treated with ET, these interactions are interrupted, which ultimately impacts the downstream signaling processes (Khattak et al. 2024).

Gamalero and Glick (2022) report that reducing soil moisture levels enhances ET metabolomic activity while concomitantly decreasing root biomass in wheat. Microbial consortia have demonstrated the capacity to mitigate levels of ACC, a precursor of ET. Notably, Enterobacter aerogenes, a bacterium associated with the rhizosheath-root system, effectively degrades ACC. This degradation process lowers ET production, subsequently promoting root biomass and rhizoplane development during water scarcity. Lee et al. (2024) underscore the significant effect of microbial consortia on ET signaling and perception within crops. Bacillus megaterium alleviates the stress induced by drought, while the Enterobacter sp. strain C7 demonstrates its influence on protein metabolism. Rhizobacteria, referred to as PGPR, can effectively alleviate stress in plants by lowering ET levels in their surrounding environments, particularly in wheat cultivation within the subtropical regions of the Indian subcontinent (Paul et al. 2024). Field trials corroborate the enhancement of agricultural production through microbial consortia in subtropical states. Lastochkina (2021) additionally identified Bacillus subtilis (LDR2) as a beneficial agent capable of mitigating ET-induced water scarcity in Trigonella plants, thereby promoting growth and alleviating biochemical shifts associated with drought.

Microbial consortia and auxin-induced reprogramming of rice plant metabolites

Auxins, crucial plant growth regulators, are synthesized and regulated by beneficial microbial consortia, including endophytic and symbiotic fungi and bacteria, especially under drought stress conditions. Microbial consortia modulate the signaling pathways and sensing mechanisms associated with plant growth regulators and metabolomics, enhancing drought tolerance and positively influencing crop growth and development. Research has shown that auxin-producing microbial consortia can significantly improve drought resilience in cereal crops, including rice, maize, and wheat. For instance, PGPRs enhance drought tolerance and improve the yield and productivity of wheat (Tanveer et al. 2024). Several rice varieties thrive in submerged conditions by promoting internode growth, regulated by the SNORKEL 1 and 2 genes, through metabolic reprogramming. Studies have highlighted the effect of metabolic reprogramming under wet and semi-dry environments, particularly in rice variety Taichung 65 (T65) (Fukushima et al. 2020). The auxin biosynthesis pathways, specifically tryptophan (Trp) and indole-3-pyruvic acid (IPyA), occur within the roots of crops, facilitating enhanced growth and development during drought by extending root length. Researchers have also elucidated the role of endophytic mycorrhizae in stimulating IAA biosynthesis through modulation and reprogramming processes, which activate a range of genes and transcription factors, ultimately leading to increased root length under drought conditions in rice. Currently, sophisticated ultra-performance liquid chromatography (UPLC) techniques are being employed to examine various reprogramming of IAA triggered by drought-tolerant and antagonistic strains of Pseudomonas fluorescens in rice. Recent findings have identified four highly efficient IAA-producing strains that positively affect rice plants. The application of bio-priming with bacterial consortia alongside auxin priming has proven beneficial in enhancing rice production under water-limited conditions. Auxins undergo modulation and reprogramming, resulting in increased concentrations of plant growth regulators and essential subcellular enzymes, such as superoxide dismutase, catalases, and peroxidases. The expression of drought-related genes and the production of plant-compatible solutes, including osmolytes, are supported by auxin-secreting microbial consortia. They promote plant development and enhance drought resistance across various cereal crops, including wheat, maize, and rice (Xu et al. 2024).

Microbial consortia influence major metabolic processes, such as photosynthesis, metabolite accumulation, and gene regulation. Rice plants adapt to drought by reducing activities through SA and JA signaling pathways, interacting with microbial consortia to influence JA levels and growth regulators. Microbial consortia also produce CK, which regulates plant growth and development. They can alleviate ACC and reduce ET production in crops, while auxins enhance drought tolerance and influence plant growth and development.

Detection of hormone production using ultra-performance liquid chromatography (UPLC)

Metabolomics is a powerful approach for analyzing biological or fermentation systems at the molecular level, focusing on understanding changes in metabolites and their functional roles. Recent studies have employed nuclear magnetic resonance (NMR) and ultra-high-performance liquid chromatography coupled with triple time-of-flight mass spectrometry (UHPLC–triple-TOF–MS/MS) to delineate metabolic profiles, identify disease biomarkers, and pinpoint potential drug targets (Barathikannan et al. 2024). UHPLC was found suitable for understanding metabolic changes and their role in antimicrobial drug discovery (Aminov 2022). Mass spectrometry (MS)-based metabolomics investigation utilizing UHPLC has illuminated the metabolic impact of monacolin K levels and various sterilization methods on Monascus-fermented rice products (MFRPs). This research has unveiled how differences in metabolites, sterilization techniques, and the use of highland barley can provide valuable insights into the health implications of MFRPs (Zhao et al. 2024a). GC–MS and 2D GC–MS techniques are applied in metabolomics involving microbial consortia and yeast systems (Almstetter et al. 2012). A comprehensive metabolomic analysis using gas chromatography–time-of-flight mass spectrometry (GC–TOF–MS) and high-performance liquid chromatography (HPLC) analyzed metabolites produced by Monascus purpureus over a 30-day period. They revealed a gradual increase in primary metabolites up to day 15, followed by a rise in secondary metabolites from day 10 onward. Notably, this study identified 23 metabolic pathways, highlighting key processes, such as glycolysis and the metabolism of pyruvate, α-linolenic acid, and linoleic acid (Kraboun et al. 2023). The application of liquid chromatography–high resolution mass spectrometry (LC–HRMS) to cereal grains—including rice, wheat, maize, and barley—underscores the critical role of untargeted metabolomics in both identifying and quantifying metabolites, as well as elucidating biochemical pathways and exploring plant defense mechanisms. Such metabolomic studies are poised to enhance rice cultivation practices, improve quality, and ultimately ensure food safety (Bozza et al. 2024). The effect of fermenting bacterial populations on the breakdown of organic materials in subseafloor sediments was examined by Glombitza et al. (2015) using IC–MS. They quantified volatile fatty acids, which are used as electron donors during the mineralization of organic materials. IC–MS has been applied to multiomic and metabolomic studies using Pseudomonas aeruginosa PAO1 (San Millan et al. 2018).

Quantitative assessment of plant growth regulators showcases their metabolic roles and reprogramming in response to abiotic stresses, such as drought, salinity, cold, and pesticide toxicity (Zhang et al. 2024b). A study evaluates the biotransformation characteristics of tetracycline by strain Serratia marcescens (MSM2304), utilizing product analysis and genomics to accurately measure plant growth regulators due to the variance in molecular and chemical properties (Wang et al. 2024b). UHPLC has established itself as a preferred separation method due to its high efficiency, resolution, speed, robustness, and widespread commercial availability. When combined with mass spectrometry (MS), it offers enhanced selectivity, sensitivity, and high-throughput capabilities for complex sample analyses, making it an ideal choice for the rapid separation and analysis of phytohormones (Kojima et al. 2009).

Recent research has led to the development of a high-throughput method for analyzing phytohormone concentrations in rice plants utilizing an automatic liquid handling system in conjunction with UPLC, a tandem quadrupole mass spectrometer, and an electrospray interface (Liu et al. 2015; Zhang et al. 2024b). The plant hormone profiling method employed in rice facilitated the creation of organ distribution maps and enabled the identification of interactions among four significant hormones within gibberellin signaling mutants (Kojima et al. 2009). This method incorporates a homemade online micro solid phase extraction (m-SPE) system paired with a UPLC–MS/MS platform. The successful quantification of both acidic and alkaline plant hormones in Ulva linza L. offers crucial insights for further investigating the physiological and ecological roles of plant hormones in lower algal species (Liu et al. 2014). Understanding plant responses to drought, including interactions with microbiomes and metabolites, is crucial for developing resilient agricultural systems. Research on plant responses, microbiome assemblages, metabolomic responses, and interactions under drought stress is ongoing, focusing on reciprocal exchange of metabolites, antioxidant enzymes, and phytohormones (Sharma et al. 2025). Quantitative measurements of these regulators are essential for understanding their metabolic functions and reprogramming. UHPLC is a prevalent separation technique used for analyzing phytohormone concentrations in both rice plants and seaweed samples, providing indispensable information for future research endeavors.

Modulation of plant proteomics by microbial consortia under symbiotic relationship under drought stress

This review examines the reprogramming of proteomics and metabolomics for a thorough understanding of plant–microbe interactions amidst drought stress. Recent studies suggest that microbial consortia have a significant impact on protein abundance, activity, and interactions, particularly during periods of reduced water availability.

Effect of AMF on plant proteomics

Microbial consortia can induce substantial changes in protein expression, signal transduction pathways, and metabolomic profiles in crops. The findings underscore the critical role of microbial consortia in plant proteomic responses under drought conditions, highlighting how native bacteria and AMF enhance growth and nutritional value. Research demonstrates that AMF and PGPR consortia significantly boost rice crop performance by elevating physiological functions, such as photosynthetic efficiency, nutrient assimilation, and overall nutrient acquisition. The exploration of plant–microbial interactions has fostered the development of consortia-based biofertilizers (Verma et al. 2024), leading to improved soil resilience and crop growth. Nevertheless, challenges persist in the formulation of crop-specific inoculants and in addressing environmental implications (Khan 2022). Moreover, these consortia provide enhanced resistance against pathogens, particularly under drought stress. AMF promote beneficial microbial consortia, assisting plants in coping with water mineral deficits. Bhatia et al. (2024) observed that mycorrhizal fungal colonization significantly promotes sorghum leaf growth and photosynthetic rates under drought conditions. Mycorrhizal plants exhibit distinct metabolic pathways during water deficits, suggesting the mediating role of microbes in plant drought responses. This acclimatization not only bolsters nutrient availability but also activates drought tolerance mechanisms (Bhatia et al. 2024). Bernardo et al. (2017) examined the role of AMF in wheat and identified changes in the regulation and reprogramming of secondary metabolites and plant growth regulators, reflecting consistent regulation of secondary metabolism. The research revealed that cereal crops positively influence sugars, lipids, metabolites related to oxidative stress, and phytohormones, underscoring the interconnected dynamics of plant–microbe–environment interactions (see Fig. 3).

Effect of endophytic bacteria on proteomic reprogramming under water stress

Studies on Barrel Clover 'Jemalong A17' and Rhizobium meliloti have analyzed plant–bacteroid components and identified 377 metabolic and proteomic reprogramming events linked to acclimatization during water scarcity, demonstrating synchronized influences within stressed symbiotic systems (Olalde-Portugal et al. 2020). Díez-Méndez and Menéndez (2021) demonstrated that microbial endophytes can activate drought tolerance mechanisms in cereal crops, including rice, thereby promoting growth even during periods of drought stress. The specific proteins triggered by endophytes enhance food assimilation processes, along with defense-related proteomes located in leaf and root cells, respectively, facilitating acclimatization to water scarcity in rice varieties. Knežević et al. (2022) explored the symbiotic relationships established by microbial consortia, particularly Microbacterium sp. 3J1, uncovering a common proteomic pathway that enhances the tolerance to water deficiency and supports the acclimatization of plants. The influence of plant microbial consortia on the proteomic landscape during drought stress is significant, affecting a range of biological processes. Further investigation is warranted to elucidate the molecular interactions involved and to identify specific microbiota species that can contribute to drought tolerance, with the ultimate goal of improving crop productivity and resilience in water-limited conditions.

This review focuses on the reprogramming of proteomics and metabolomics to deepen our understanding of plant–microbe interactions under drought stress. Plant microbial consortia influence protein abundance, activity, and interactions, particularly in scenarios of water scarcity. These consortia can induce modifications in protein expression, signal transduction pathways, and metabolomic profiles in crops. AMF and PGPR enhance the growth of rice. These consortia are capable of developing biofertilizers and improving plant resistance against pathogens.

Modulation of plant metabolomics by microbial consortia under water scarcity

Metabolomics is a crucial technology for analyzing and quantifying secondary metabolites, enhancing our understanding of chemical signaling and regulatory systems across various plant species (Khan et al. 2023). It aids in identifying and quantifying genomic and environmental variations, elucidating morphological, genotypic, and mutagenic plant characteristics, and antagonistic properties, contributing to medicinal development . Metabolomics also promotes resistance to biotic and abiotic stresses (Razzaq et al. 2019; Meraj et al. 2020). Advancements in signal transduction pathways are responsible for biosynthesis. Researchers have implemented omics techniques to improve crop varieties, particularly those with high yield potential (Ashraf et al. 2022). Advanced metabolomic techniques can develop crop varieties with superior yields, exhibiting structural, biochemical, and Functional variations critical to plant growth and increased agricultural productivity. Microbial consortia activate signaling and sensing pathways involving over 1000 metabolites (Sena et al. 2024). Microbial consortia, a specialized group of microbial communities frequently residing interdependently, significantly influence plant responses to drought stress, thereby affecting the synthesis of a range of metabolites and enhancing plant resilience to environmental stressors, particularly within the rhizosphere and endosphere.

Ascorbate–glutathione cycle in the modulation of plant metabolomics

The pathway undergoes multiple interactions among ascorbate (AsA), glutathione (GSH), and enzymes ascorbate peroxidase (APX), glutathione reductase (GR), monodehydroascorbate reductase (MDHAR), and dehydroascorbate reductase (DHAR). Peng et al. (2024) and Chen et al. (2024c) demonstrated that the combined application of microbial consortia and silicon can increase the synthesis of detoxifying enzymes and further explore the AsA-GSH cycle in Glycyrrhiza uralensis.

Oxidative phosphorylation and phenylalanine metabolism in the modulation of plant metabolomics

Oxidative phosphorylation produces ATP, which is essential for phenylalanine metabolism and other metabolic processes. Dejana (2023) investigated the drought resilience of walnut roots in relation to AMF, assessing its effect on biomass enhancement and leaf water retention under water-limited conditions, with implications for critical pathways, such as oxidative phosphorylation and phenylalanine metabolism. The study highlighted the interconnections of these metabolic processes under water stress. A study analyzed the metabolic activities of salt-stressed flag leaf rice plants using transcriptomics and metabolomics data. It reported metabolic reprogramming in primary pathways, cellular respiration, antioxidant biosynthetic pathways, and phytohormone biosynthetic pathways. Photosynthesis and hexose utilization were disturbed, suggesting increased flux distribution of the photorespiratory pathway that could contribute to cellular redox control (Wanichthanarak et al. 2020). PGPRs, such as Trichoderma viride and Pseudomonas fluorescens, are essential for nutrient cycling, soil microbiome restructuring, signaling compounds, and plant growth management (Kumar et al. 2023). They stimulate growth, control pathogens, and manage abiotic stress. Some PGPRs perform biocontrol through siderophore production. Phenylalanine ammonia-lyase (PAL) is essential for the biosynthesis of SA, a signal involved in induced systemic resistance, and defense-related secondary compounds, such as phenols and lignin. Trichoderma can induce plant resistance by increasing enzyme activity in rice leaves (Islam et al. 2023).

ABA and JA singalling pathways in the modulation of plant metabolomics

ABA and JA pathways are crucial plant hormonal pathways that interact with each other under stress conditions. Microbial consortia facilitate enhanced excretion of amino acids through the roots of rice plants during water scarcity through modifications in bacterial composition, and fluctuations in levels of ABA and JA. An assortment of microbial consortia is associated with various organic compounds and amino acid mucilages (Li et al. 2024).

GS-GOGAT pathway in the modulation of plant metabolomics

Vílchez et al. (2018) investigated how drought-induced metabolic alterations relate to esca disease in grapevine trunk disease. They found that water stress notably elevates metabolite concentrations, emphasizing the critical role of plant–microbe interactions. Interactions among microbial consortia and the plants significantly contribute to metabolomic changes during water scarcity. The potential for microbial consortia to activate defense mechanisms in cereal crops, including wheat and rice, under water stress was elucidated by Camaille et al. (2021). They outlined the importance of understanding microbial dynamics and crop metabolomics for advancing sustainable agriculture. An outline illustrating the synergistic effects of microbial consortia on rice plants in response to both biotic and abiotic stressors is presented in Fig. 4. Microbial consortia can suppress plant diseases by triggering changes in Branched Chain Amino Acid (BCAA) metabolism in rice. They increase the amount of BCAA amino acids in panicles and rice grains by activating the OsAUX5 gene. These amino acids influence the GS–GOGAT pathway to enhance the synthesis of primary and secondary metabolites, triggering the defense system under biotic and abiotic stress (Fig. 4). This encompasses the activation of defense systems, modulation of phytohormone levels, and adjustments in metabolic profiles, alongside enhancements in root development and nutrient uptake within the rice rhizosphere. Ali and Khan (2021) explored rhizobacterial priming as a method to bolster drought resistance in sorghum. They identified beneficial species such as Bacillus and Pseudomonas that feature ACC deaminase dismutase activity, which serves a protective function against abiotic stresses, particularly drought. Priming boosts plant resilience to drought-induced water stress. It enhances antioxidant capacities, upregulates hormone levels, activates tolerance and signaling molecules, and generates osmolytes, collectively contributing to the lowering of ET levels, presenting a valuable strategy for sustainable agriculture. These studies reveal the intricate relationship between microbial consortia and the reprogramming of plant metabolomics in conditions of water scarcity. The study advances our understanding to promote sustainable agricultural strategies amidst the challenges posed by climate change and limited water resources.

Fig. 4.

Microbial consortia play a crucial role in suppressing plant diseases by modulating hormonal signaling and triggering changes in Branched Chain Amino Acids (BCAA) metabolism in rice plants. They increase the amount of valine, leucine, isoleucine, tyrosine, tryptophan, tryptamine, and alanine in panicles and rice grains by activating the OsAUX5 gene in rice. Among the BCAA amino acids, leucine, isoleucine, and valine play a key role in the completion GS–GOGAT pathway and enhance the synthesis of primary and secondary metabolites, which trigger the defence system under biotic and abiotic stress. Microbial consortia also trigger multiple signalling cascades such as Jasmonic acid and salicylic acid signalling pathway in rice plants through the modulation of phytohormones, such as nitic oxide, abscisic acid, ethylene, cytokinin, gibberellic acid, and auxin, along with modulation in secondary metabolites such as phenolic compounds, terpenes, carotenoides and flavonoids under drought stress in rice plants. CoA Coenzyme A; CoASH Reduced coenzyme A, TPP Thiamine pyrophosphate, FADH Flavin adenine dinucleotide (semi-reduced), FADH₂ Reduced flavin adenine dinucleotide, NADH Nicotinamide adenine dinucleotide (reduced)

Plant–microbe interactions significantly influence the signaling, and sensing cascades initiated by SA and JA (Nadarajah et al. 2021). These pathways modulate various proteins and hormonal mechanisms, including those involving ABA, CK, ET, and auxins, particularly under drought conditions and biotic stresses affecting rice plants (Li et al. 2017; Rosier et al. 2018; Ngoune and Shelton 2020). Fluctuations in environmental conditions pose substantial challenges to the cultivation of field crops, notably rice. This crop is particularly sensitive to climate change factors, such as drought, heat stress, salinity, cold stress, and pesticide toxicity (Raza et al. 2020). Among these abiotic stresses, drought emerges as a primary challenge for rice cultivation in semi-rainfed, dry, and rainfed systems. Addressing these challenges requires harnessing primary plant metabolites, including phenolics, lignin, and phytohormones, alongside enhancing the synthesis of phytoalexins, pathogenesis-related (PR) proteins, and the generation of ROS within the cellular components of rice (Vigani et al. 2016; Aguirre-Becerra et al. 2021).

Metabolomics, an emerging technology, facilitates the identification and quantification of secondary metabolites while enhancing our understanding of chemical signaling and systemic interactions in various plant groups. This technology is essential for developing medicines, identifying and alleviating abiotic stresses, and breeding for resistance and drought tolerance in cereal crops, such as rice and wheat. Metabolomics is pivotal in elucidating plant–microbe interactions and examining the links between drought-related metabolic changes and disease epidemiology.

Microbial consortia for plant protection and soil–plant health: implications for drought resilience

A metabolomic study comparing postbiotics from three lactic acid bacteria strains and rice bran found that these postbiotics suppressed Salmonella typhimurium by 42–55% more effectively than probiotic-only counterparts. This study identified 109 metabolites under postbiotics, suggesting that variations in postbiotic antimicrobial activity are crucial for developing adjunctive treatments against pathogens (Nealon et al. 2024). Microbial consortia, such as endophytic AMF (Fernandez and Wilson 2014), can enhance plant resilience against adverse environmental conditions, particularly during drought and heat stress (Villalobos-López et al. 2022). They maintain nitrogen balance, optimize the GS–GOGAT pathway, improve rice crop yields while preserving soil health and facilitating the reclamation of toxic metallic compounds (Wang, Mostafa et al., 2021b; Emenike et al. 2023).

Endophytic AMF, Pseudomonas fluorescens, and Trichoderma harzianum also detoxify residual contaminants such as 2–4-D and zinc phosphite through oxidation and reduction processes in affected soils (Bhadrecha and Bhawana 2023). These consortia enhance the availability of essential nutrients, increasing nitrogen and phosphorus levels in the soil and converting insoluble phosphorus into more accessible forms while facilitating nitrogen fixation (Zhou and Xu 2023). These consortia can be optimized by modulating drought-responsive genes, improving nutrient availability, providing protection against biotic stress, and enhancing resilience to drought conditions (Zia et al. 2021). This is accomplished through the activation of various signaling and sensing pathways, including hormonal signaling and free-radical scavenging, which help plants to mitigate the adverse impacts of drought stress, particularly in rice (Poudel et al. 2021). Recent studies highlight that soil aerobic CH₄ oxidation supports denitrification in paddy fields, demonstrating a metabolic coupling between methanotrophs and denitrifying bacteria. A ¹³C metabolomics analysis identified over 70 phylotypes with genes connected to denitrification and ¹³C assimilation, underscoring the significance of metabolic intermediates, such as acetate, lactate, and propionate (Chen et al. 2024a). Microbial consortia address various stresses through diverse acclimatization strategies, including soil percolation and defense against drought. Microbial synthetic biology applications are becoming complex due to large genetic circuits. Microbial consortia are required to distribute complex tasks among multiple populations using mutualistic interactions, population control, and spatial segregation strategies. The rice microbiome plays a crucial role in plant health and nutrient acquisition, regulating nutrient cycling, growth promotion, and stress resistance (Misu et al. 2025). Recent molecular biology research has revealed complex interactions within rice microbiomes, essential for sustainable production and environmental health. Advances in microbiome engineering optimize nutrient availability and resilience to abiotic stresses. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes offer promising solutions.

Conclusion and future prospects

Microbial consortia are capable of mitigating various stresses, including drought stress, through various mechanisms. This complex interaction involves an array of micro-organisms, such as fungi, bacteria, and viruses, which contribute to the reprogramming of both primary and secondary metabolites in plants. These changes enhance the plants' defenses against drought, stimulate signaling pathways regulated by plant growth substances, and counteract drought-related pathogens. Under drought conditions, plants exhibit a range of adaptive responses, adjusting their chemical, biochemical, and molecular activities, as well as their cellular and phenotypic traits. The interplay between microbial communities and the reconfiguration of plant metabolites in response to water scarcity has provided valuable insights for developing sustainable agricultural practices in light of water shortages and climate challenges. Recent advancements in analytical techniques, such as UPLS/GC, have improved our ability to profile and quantify the impact of microbial consortia on plant growth regulators under drought conditions. These microbial interactions significantly alter the proteomic profile of plants experiencing drought stress, affecting numerous physiological processes. Drought stress mitigation can be achieved through various mechanisms. These mechanisms are improved nutrient acquisition, phytohormone production, systemic acquired resistance, antioxidant enzyme induction, osmolyte accumulation, and exopolysaccharide production. Key microbial consortia candidates include nitrogen-fixing bacteria, such as Rhizobium, Azotobacter, Azospirillum, Bacillus, Pseudomonas, and Enterobacter. They convert atmospheric nitrogen into available forms for plants. Phosphate-solubilizing bacteria, such as Bacillus and Pseudomonas, solubilize insoluble phosphate in the soil, making it accessible to plants. Mycorrhizal fungi form symbiotic relationships with plant roots, enhancing nutrient and water uptake. Other plant growth-promoting rhizobacteria, such as auxins, cytokinins, and gibberellins, produce phytohormones that promote root growth and nutrient uptake. Pseudomonas can also produce siderophores, which chelate iron, making it available to plants under iron-limiting conditions. Bacterial consortia can biofortify crops with nutrients, such as zinc. Phytohormone production regulates plant growth processes, while systemic acquired resistance is a defense mechanism used by plants to resist pathogens and abiotic stresses, like drought. Lactic acid bacteria, Xanthomonas, and Bacillus can produce exopolysaccharides or biopolymers, commonly used in industrial applications. They can improve soil aggregation, water retention, and nutrient availability, creating a more favorable environment for plant growth under drought conditions.

Further investigation is necessary to elucidate the molecular relationships and to pinpoint specific microbial candidate species that enhance drought tolerance. Such understanding is crucial for increasing crop yields and resilience in environments facing water limitations. In addition, metabolomics technology serves as a powerful tool for identifying and quantifying secondary metabolites, facilitating insights into chemical signaling and regulatory systems across diverse plant species. This approach not only develops medicinal compounds but also mitigates abiotic stresses and breeds resilient varieties capable of withstanding drought, particularly in rice and wheat. A comprehensive understanding of microbial dynamics and plant metabolomics is key to advancing sustainable agricultural practices.

Ethical approval

Ethical issues are not applicable to this review article. This paper does not involve a study on animals.

Author contributions

Ajay Tomar (AT), Chitranjan Kumar (CK), Kshitij Parmar (KP), Naeem Khan (NK), Ramji Singh (RJ), Sunil Kumar Dwivedi (SKD), and Durga Prasad proposed the idea and topic of this research. AT and CK originally wrote this paper. NK, RJ, SKD, and DP revised this paper. All authors have seen the final version of this manuscript.

Data availability

The data mentioned in the article will be made available upon a request.

Declarations

Conflict of interest

The authors declare that there is no conflict of interest among authors for the publication of this manuscript in this journal.